Graham O'Hara

Deep sand soils are inherently fragile with surface layers that are very low in organic matter and clay. Previous studies demonstrate that strategic deep tillage such as soil inversion and deep soil mixing can increase crop production on these soils in Southern Australia. However, the majority of the organic matter and nutrients are concentrated in the top organically stained layer and deep tillage incorporates 50-60 % of the organic layer into the subsoil below 200 mm. The physical composition of the soil (percentage of sand, silt, clay and organic matter) and the chemical properties of the soil (pH, nutrient levels, cation exchange capacity) can strongly influence the soil adsorption of trifluralin. Modest levels of organic matter and clay particles in the topsoil particularly following deep tillage equate to the scant attenuation of herbicides on sandy textured soils. Soil samples (0-100 mm) were collected from three experimental sites; two Arenic Solonetz soils near Esperance and one Arenic Arenosol soil near Geraldton in Western Australia. At all three sites, three experimental treatments were sampled; control (no tillage), deep mixed with a spader to 350 mm and soil inversion with a mouldboard plough to 350 mm. Soil samples were taken on two growing seasons post tillage at Geraldton, three post tillage at Esperance TJM and twelve post tillage at Esperance E1. Tillage reduced the measured soil-liquid partition coefficient (Kd) of trifluralin (p <= 0.05) at all three experimental sites. A greenhouse bioassay was developed to determine if soil changes from strategic tillage at one of the Esperance sites and the Geraldton site could be directly related to herbicide bioavailability at two of the experimental sites. Intact cores were used to maintain integrity of the field soils. Cores from both field sites demonstrated that soil inversion reduced the effective dose of trifluralin (p <0.01) for the bioassay species Lens culinaris. Together these experiments illustrate that strategic deep tillage can increase the bioavailability of trifluralin. These findings offer a valuable insight into the soil behaviour of trifluralin and can help farmers estimate the risk of phytotoxicity based on measurable soil characteristics.

Physical dormancy in seeds is caused by a water-impermeable seed coat. It plays a crucial role in the sustainability of ley farming systems in Mediterranean climates by enabling pasture legumes to regenerate from a soil seed bank. Sophisticated management of the pattern of physical dormancy break can synchronize germination of plants with the optimal growing season, essential to the sustainability of the system. The ability of the maternal plant to reproduce and provide its progeny (seed) with sufficient resources is influenced by both genetic and environmental factors. However, when abiotic (e.g., drought, temperature) or biotic (e.g., pests, diseases) stressors affect the maternal plant during its reproductive phase, the allocation of resources to seeds can vary, leading to variability in physical dormancy outcomes. This genetic × environment interaction is well documented; however, a third factor, management, is less understood. Herein lies a significant knowledge gap, and this is the first review that examines physical dormancy from an agricultural management perspective. In the manuscript, we explore the evolution of physical dormancy in pasture legumes in ley farming systems and how the intensification of agricultural management practices inadvertently affects physical dormancy development and the pattern of release. This intensification threatens the sustainability of ley farming by changing the timing of physical dormancy release, which concomitantly occurs under changed climatic conditions. Therefore, climate change combined with the intensification of agricultural management practices, including pesticide use, altered grazing regimes, and frequency of crop rotation, poses significant challenges to physical dormancy regulation and soil seed bank dynamics in ley farming. We suggest that to combat the impacts of agricultural intensification, detailed studies and breeding programs should focus on selecting legumes with both agricultural and climatic resilience for successful adaptation to evolving agricultural landscapes and ensure continued sustainable productivity.

Rhizobia are soil bacteria capable of establishing symbiosis within legume root nodules, where they reduce atmospheric N2 into ammonia and supply it to the plant for growth. Australian soils often lack rhizobia compatible with introduced agricultural legumes, so inoculation with exotic strains has become a common practice for over 50 years. While extensive research has assessed the N2-fixing capabilities of these inoculants, their genomics, taxonomy, and core and accessory gene phylogeny are poorly characterized. Furthermore, in some cases, inoculant strains have been developed from isolations made in Australia. It is unknown whether these strains represent naturalized exotic organisms, native rhizobia with a capacity to nodulate introduced legumes, or recombinant strains arising from horizontal transfer between introduced and native bacteria. Here, we describe the complete, closed genome sequences of 42 Australian commercial rhizobia. These strains span the genera, Bradyrhizobium, Mesorhizobium, Methylobacterium, Rhizobium, and Sinorhizobium, and only 23 strains were identified to species level. Within inoculant strain genomes, replicon structure and location of symbiosis genes were consistent with those of model strains for each genus, except for Rhizobium sp. SRDI969, where the symbiosis genes are chromosomally encoded. Genomic analysis of the strains isolated from Australia showed they were related to exotic strains, suggesting that they may have colonized Australian soils following undocumented introductions. These genome sequences provide the basis for accurate strain identification to manage inoculation and identify the prevalence and impact of horizontal gene transfer (HGT) on legume productivity.

IMPORTANCE: Inoculation of cultivated legumes with exotic rhizobia is integral to Australian agriculture in soils lacking compatible rhizobia. The Australian inoculant program supplies phenotypically characterized high-performing strains for farmers but in most cases, little is known about the genomes of these rhizobia. Horizontal gene transfer (HGT) of symbiosis genes from inoculant strains to native non-symbiotic rhizobia frequently occurs in Australian soils and can impact the long-term stability and efficacy of legume inoculation. Here, we present the analysis of reference-quality genomes for 42 Australian commercial rhizobial inoculants. We verify and classify the genetics, genome architecture, and taxonomy of these organisms. Importantly, these genome sequences will facilitate the accurate strain identification and monitoring of inoculants in soils and plant nodules, as well as enable detection of horizontal gene transfer to native rhizobia, thus ensuring the efficacy and integrity of Australia’s legume inoculation program.

Background and aims
Mesorhizobium ciceri CC1192 is the commercial inoculant strain for Cicer arietinum (chickpea) cultivation in Australia, including in the Ord River Irrigation Area (ORIA), where C. arietinum cropping began in 1985. Mesorhizobium strains are known to gain the capacity to nodulate legumes through acquisition of symbiosis Integrative and Conjugative Elements (ICEs), leading to the evolution of novel rhizobia. Here, we assess the impact of symbiosis ICE transfer and compare the genomic diversity and symbiotic effectiveness of C. arietinum nodulating rhizobia from the ORIA.

Methods
Nodule isolates collected from field cultivated C. arietinum were genotyped by RAPD-PCR, and representative strains from each genotype were whole genome sequenced and symbiotically phenotyped in glasshouse conditions to assess N2 fixation effectiveness against CC1192.

Results
A total of 68 nodule isolates, all harbouring the CC1192 symbiosis ICE (ICEMcSym1192), were analysed, with 12 identified as the inoculant strain, and 56 novel strains clustering into ten genotypes. These novel genotypes dominated as nodule occupants across the majority of sites sampled. Nine of the ten representative strains were as effective at N2 fixation as CC1192, with WSM4904 the only ineffective strain. Core genome phylogeny showed the ten strains represent four novel Mesorhizobium genospecies. Novel strains WSM4904 and WSM4906 shared 98.7% sequence identity, yet exhibited very different symbiotic phenotypes.

Conclusions
The CC1192 symbiosis ICE has transferred to a wide diversity of Mesorhizobium spp. in the ORIA. These evolved strains are competitive against CC1192 at nodulating C. arietinum, and the majority are effective symbiotic N2 fixers.

Rhizobia are a diverse group of α- and β-proteobacteria that boost soil fertility by forming a nitrogen-fixing symbiosis with legumes, which is why legumes are grown in rotation with cereals in agriculture. Rhizobia that naturally populate Australian soils are largely incompatible with exotic agricultural legumes, therefore, compatible strains have been imported from all over the world for use as inoculants. An amalgamated collection of these strains, called the International Legume Inoculant Genebank (ILIG), has been established at Murdoch University, to provide a centralised strain storage facility and support rhizobial research and inoculant development (see http://ilig.murdoch.edu.au). The ILIG contains 11,558 strains representing 96 bacterial species from 778 legume species collected from >1200 locations across 100 countries. New and sometimes inefficient rhizobia evolve in the field following legume inoculation, through horizontal symbiosis gene transfer from inoculants to soil bacteria. To provide a benchmark to monitor and assess the impact of this evolution, all commercial Australian inoculant strains were genome sequenced and these data made available (PRJNA783123, see https://www.ncbi.nlm.nih.gov/bioproject/PRJNA783123/). These data, and the further sequencing of the >11,000 historical strains in the ILIG, will increase our understanding of rhizobial evolution and diversity and provide the backbone for efforts to safeguard Australia’s legume inoculation program.

Growing a high-value crop such as industrial hemp (Cannabis sativa L.) in post-mining environments is economically and environmentally attractive but faces a range of biotic and abiotic challenges. An opportunity to investigate the cultivation of C. sativa presented itself as part of post-mining activities on Christmas Island (Australia) to profitably utilise disused phosphate (PS) quarries. Challenges to plant growth and cadmium (Cd) uptake were addressed in this study using potted plants under fully controlled conditions in a growth chamber. A complete nutritional spectrum, slow-release fertiliser was applied to all plants as a control treatment, and two levels of rock PS dust, a waste product of PS mining that contains 35% phosphorus (P) and 40 ppm of naturally occurring Cd, were applied at 54 and 162 g L−1. After 12 weeks, control plants (no PS dust) significantly differed in phenological development, with no flower production, lower aboveground biomass and reduced photosynthesis efficiency than those with P applied as rock dust. Compared with the controls, the 54 g L−1 level of P dust increased shoot biomass by 38%, while 162 g L−1 increased shoot biomass by 85%. The concentration of Δ9-tetrahydrocannabinol also increased with the higher P levels. Cd uptake from PS dust by C. sativa was substantial and warrants further investigation. However, there was no increase in Cd content between the 54 and 162 g L−1 application rates in seed and leaf. Results indicate that hemp could become a high-value crop on Christmas Island, with the readily available rock PS dust providing a source of P.

The vacuolar processing enzyme gene TaVPE3cB is identified as a candidate gene for a QTL of wheat pith-thickness on chromosome 3B by BSR-seq and differential expression analyses. The high pith-thickness (PT) of the wheat stem could greatly enhance stem mechanical strength, especially the basal internodes which support the heavier upper part, such as upper stems, leaves and spikes. A QTL for PT in wheat was previously discovered on 3BL in a double haploid population of 'Westonia' × 'Kauz'. Here, a bulked segregant RNA-seq analysis was applied to identify candidate genes and develop associated SNP markers for PT. In this study, we aimed at screening differentially expressed genes (DEGs) and SNPs in the 3BL QTL interval. Sixteen DEGs were obtained based on BSR-seq and differential expression analyses. Twenty-four high-probability SNPs in eight genes were identified by comparing the allelic polymorphism in mRNA sequences between the high PT and low PT samples. Among them, six genes were confirmed to be associated with PT by qRT-PCR and sequencing. A putative vacuolar processing enzyme gene TaVPE3cB was screened out as a potential PT candidate gene in Australian wheat 'Westonia'. A robust SNP marker associated with TaVPE3cB was developed, which can assist in the introgression of TaVPE3cB.b in wheat breeding programs. In addition, we also discussed the function of other DEGs which may be related to pith development and programmed cell death (PCD). A five-level hierarchical regulation mechanism of stem pith PCD in wheat was proposed.

Background and Aims

Inoculation of legumes with effective N2-fixing rhizobia is a common practice to improve farming profitability and sustainability. To succeed, inoculant rhizobia must overcome competition for nodulation by resident soil rhizobia that fix N2 ineffectively. In Kenya, where Phaseolus vulgaris (common bean) is inoculated with highly effective Rhizobium tropici CIAT899 from Colombia, response to inoculation is low, possibly due to competition from ineffective resident soil rhizobia. Here, we evaluate the competitiveness of CIAT899 against diverse rhizobia isolated from cultivated Kenyan P. vulgaris.

Methods

The ability of 28 Kenyan P. vulgaris strains to nodulate this host when co-inoculated with CIAT899 was assessed. Rhizosphere competence of a subset of strains and the ability of seed inoculated CIAT899 to nodulate P. vulgaris when sown into soil with pre-existing populations of rhizobia was analyzed.

Results

Competitiveness varied widely, with only 27% of the test strains more competitive than CIAT899 at nodulating P. vulgaris. While competitiveness did not correlate with symbiotic effectiveness, five strains were competitive against CIAT899 and symbiotically effective. In contrast, rhizosphere competence strongly correlated with competitiveness. Soil rhizobia had a position-dependent numerical advantage, outcompeting seed-inoculated CIAT899 for nodulation of P. vulgaris, unless the resident strain was poorly competitive.

Conclusion

Suboptimally effective rhizobia can outcompete CIAT899 for nodulation of P. vulgaris. If these strains are widespread in Kenyan soils, they may largely explain the poor response to inoculation. The five competitive and effective strains characterized here are candidates for inoculant development and may prove better adapted to Kenyan conditions than CIAT899.

To improve the yield and quality of wheat is of great importance for food security worldwide. One of the most effective and significant approaches to achieve this goal is to enhance the nitrogen use efficiency (NUE) in wheat. In this review, a comprehensive understanding of the factors involved in the process of the wheat nitrogen uptake, assimilation and remobilization of nitrogen in wheat were introduced. An appropriate definition of NUE is vital prior to its precise evaluation for the following gene identification and breeding process. Apart from grain yield (GY) and grain protein content (GPC), the commonly recognized major indicators of NUE, grain protein deviation (GPD) could also be considered as a potential trait for NUE evaluation. As a complex quantitative trait, NUE is affected by transporter proteins, kinases, transcription factors (TFs) and micro RNAs (miRNAs), which participate in the nitrogen uptake process, as well as key enzymes, circadian regulators, cross-talks between carbon metabolism, which are associated with nitrogen assimilation and remobilization. A series of quantitative genetic loci (QTLs) and linking markers were compiled in the hope to help discover more efficient and useful genetic resources for breeding program. For future NUE improvement, an exploration for other criteria during selection process that incorporates morphological, physiological and biochemical traits is needed. Applying new technologies from phenomics will allow high-throughput NUE phenotyping and accelerate the breeding process. A combination of multi-omics techniques and the previously verified QTLs and molecular markers will facilitate the NUE QTL-mapping and novel gene identification.